2CQZ
Crystal Structure of PH0347 protein from Pyrococcus horikoshii OT3
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 9 | 295 | Sodium chloride, Bicine, PEG-MME 550, pH 9.0, microbatch, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 44.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.511 | α = 90 |
b = 101.166 | β = 119.78 |
c = 78.646 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS | 2005-04-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | 1.0 | SPring-8 | BL26B1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.6 | 50 | 99.7 | 0.057 | 9 | 3.6 | 32523 | 32607 | 46.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.6 | 2.69 | 98.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1XX7 | 2.6 | 40 | 32607 | 32523 | 1616 | 99.66 | 0.195 | 0.195 | 0.195 | 0.22531 | RANDOM | 39.287 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.68 | -0.69 | 3.74 | -2.75 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 5.83 |
r_scbond_it | 3.511 |
r_mcangle_it | 2.036 |
r_dihedral_angle_1_deg | 1.973 |
r_angle_refined_deg | 1.542 |
r_mcbond_it | 1.022 |
r_symmetry_vdw_refined | 0.332 |
r_nbd_refined | 0.253 |
r_symmetry_hbond_refined | 0.236 |
r_xyhbond_nbd_refined | 0.193 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8448 |
Nucleic Acid Atoms | |
Solvent Atoms | 171 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
EPMR | phasing |